The problem is that you are not tracking the files locally but identical files are tracked remotely so in order to "pull" your system would be forced to overwrite the local files which are not version controlled.

Try running

git add *
git stash
git pull

This will track all files, remove all of your local changes to those files, and then get the files from the server.

Email codedump link for The following untracked working tree files would be overwritten by merge, but I don&#39;t care